I'm not sure how people deal with the disappearing scroll bars if they don't have a scroll-wheel mouse. For me the missing bars are fine because I can make them reappear at any time by lightly touching the scroll wheel.
They are also surprisingly nice for the column views on Mac OS X (an interface that basically consisted of a horizontal scroll bar over a range of several vertical-scrolling lists). Now, without scroll bars, the column views look so much more sensible; before they seemed to be littered with chrome.
I don't think scroll bars should disappear completely though. It seems that muting them (e.g. becoming light gray and translucent, or thinner like they are on Linux) would be enough to keep them out of the way.
It would also help if there were some additional cue, e.g. a "fade-out" effect at the edges where more content is available offscreen.